NGS-PrimerPlex v1.3.4

The bug for primers that are located near the start of the reference sequence was fixed. Primers were designed normally and the sequence was correct, but the amplicon's start and end were incorrect. For primers that were not near the start of reference sequence (further than maximal amplicon length, e.g. all cases for whole human genome), the coordinates were correct.

NGS-PrimerPlex v1.3.3

Fixed very important bug! For right primers additional analysis for hairpins, dimers, and opportunity to replace T with U was not carried out. The internal analysis of primer3 was performed normally.

NGS-PrimerPlex v1.3.2

Fix bug with good names in graphs while sorting to multiplexes

NGS-PrimerPlex v1.3.1

Some bugs were fixed

NGS-PrimerPlex v1.3.0

Several important improvements were made:

• Now users can add uridines into primers! Two parameters control their location: -umaxtm (the maximal acceptable Tm for Tm of primer parts left after primer cleavage by uridine) and -unucs (number of nucleotides from 3'-end of primer in which one T should be replaced with U. The 2nd U is inserted in the left part of primer in such a way that Tm for two parts is maximally equal. By default, T is not replaced with U at all)
• Users can skip bad primers that do not correspond to new parameters, and new versions will be designed for them!
• Non target amplicons are written to 2nd worksheet in the all_internal_primers_specificity.xls file.
• Primers that form very stable dimers (controlled by the -minmultdimerdg2 argument) are not allowed even in different multiplexes!
• Primers that can be joined into one block are saved into new type of draft primers - all_draft_primers_after_joinment.xls. Primers that are thought to prevent this joinment are excluded.
• Some bugs were fixed.

NGS-PrimerPlex v1.2.2

Parallelization was changed from the ThreadPool to the Pool of the multiprocessing. Logging was improved:

• Reasons why primers couldn't be designed are more detailed;
• The progress of reading draft-file was added;

Some bugs were fixed:

• Bug with extracting gene coordinates for bacterial genomes (they don't have mRNA tags in GB-files)
• Bugs with running GUI (e.g. when due to Docker issues in Windows list of images cannot be received)

Wiki was improved

NGS-PrimerPlex v1.2.1

The following significant bug was fixed:
while reading SAM-file with non-target hybridization sites sometimes strand value was changed. This led to the incorrect non-target region sequence extraction from a genome

NGS-PrimerPlex v1.2

The following updates were done:
Bug of detecting non-target regions fixed
Tests improved (tests by output format and checking primers for SNPs and non-targets)
Bugs of primer design for short chromosomes (e.g. for viruses) fixed
Code of extracting genome regions improved
Bug with internal filtering primers fixed
All bugs fixed were not critical for previous versions, although improve NGS-PrimerPlex performance.

NGS-PrimerPlex v1.1

GUI-version and non-human organism genomes
In the new version of NGS-PrimerPlex the program can be run in GUI. Some bugs for using organisms other than human were fixed. Now all commands don't require internet-connection. Earlier checking for SNPs and getting chromosome name for a gene did require. They were replaced with reading dbSNP VCF-file and one-time reading all GenBank-files with extraction of all gene names, respectively.

NGS-PrimerPlex v1.0

This is a first release of NGS-PrimerPlex. It can do everything that is claimed in the README file.
In future versions the following updates are planned:

• function that writes list of unspecific products into file
• function that reads list of unspecific products from file
• arguments which will get chromosome numbers that match some chromosomes as letters (e.g. X - 23; Y - 24) for other organisms